Differential Chromatin Interaction

Do the DCI(differential chromatin interaction) analysis between two Hi-C matrics. The Selfish method used here is described in the paper:

Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi, Selfish: discovery of differential chromatin interactions via a self-similarity measure, Bioinformatics, Volume 35, Issue 14, July 2019, Pages i145–i153, https://doi.org/10.1093/bioinformatics/btz362

https://github.com/ay-lab/selfish/raw/master/demo.png 
[1]:

import coolbox
from coolbox.api import *

[2]:

coolbox.__version__

[2]:

'0.3.0'

[3]:

data_dir = "../../../tests/test_data/"
cl1 = f"{data_dir}/cool_chr1_89000000_90400000_for_cmp_1.mcool"
cl2 = f"{data_dir}/cool_chr1_89000000_90400000_for_cmp_2.mcool"

region = "chr1:89237500-90227500"

The Selfish track input two hic track(Cool or DotHiC), it perform the selfish algorithm on the local fetched matrics. Output the q-value(p-value after fdr_bh correction) of differential interaction analysis:

[4]:

with MinValue(-9), MaxValue(-1):
    cool1 = Cool(cl1)
    cool2 = Cool(cl2)

frame = XAxis() + \
    cool1 + \
    cool2 + \
    Selfish(cool1, cool2, norm="log") + \
    XAxis()
frame *= Feature(depth_ratio=0.35)
frame.plot(region)

[4]:
../_images/_gallery_selfish_5_0.png

CLI code

[5]:

%%bash

data_dir="../../../tests/test_data/"
cl1="${data_dir}/cool_chr1_89000000_90400000_for_cmp_1.mcool"
cl2="${data_dir}/cool_chr1_89000000_90400000_for_cmp_2.mcool"

coolbox add XAxis - \
start_with Feature --depth_ratio="0.35" - \
    start_with Feature --min_value="-9" --max_value="-1" - \
        add Cool $cl1 - \
        add Cool $cl2 - \
    end_with - \
    add Selfish $cl1 $cl2 --norm 'log' - \
end_with - \
add XAxis - \
goto "chr1:89237500-90227500" - \
plot /tmp/test_coolbox_selfish.png